The Global Positioning System (GPS) coordinates of each GCP must be collected so they can be used in PhytoOracle workflows. To accomplish this, you need a Trimble Global Navigation Satellite System (GNSS) (Figure @ref(fig:trimbleplot)).
Trimble Global Navigation Satellite System (GNSS) used to collect accurate Global Positioning System (GPS) coordinates of Ground Control Points (GCPs).
The United States Department of Agriculture (USDA) Arid Land Agricultural Research Center (ALARC) has trimbles that we can borrow. To use them, follow the steps below:
Run Trimble Access - Press Trimble hard key (Windows symbol), select Trimble Access
Log in — Click either “Tap here to log in” or the current logged in person (e.g., kelly.thorp)
PhytoOracle relies on geospatial information, such as GPS coordinates, to accurately link phenotypes with a location in the field. This allows us to detect, tag, and track individual plants over the course of multiple Field Scanalyzer scans. Specifically, PhytoOracle requires two files:
These files must be generated prior to data processing for the respective season. Additionally, these files should be loaded onto QGIS for visual inspection and confirmation that the coordinates are accurate.
The Trimble collects GPS coordinates in the Easting, Northing format (Table @ref(tab:trimbledatatable)). PhytoOracle requires GPS coordinates to be in the latitude, longitude format. To convert the coordinates, use the gcp_coordinates_conversion repository to use the conversion tool. After running the conversion script, the data will now be in the required latitude, longitude format (Table @ref(tab:gcpfiletable)).
| GCP | Type | Northing | Easting | Height..m. |
|---|---|---|---|---|
| plate1 | White | 3659979 | 408992.8 | 360.775 |
| plate2 | White | 3659987 | 408992.9 | 360.788 |
| plate3 | White | 3659995 | 408992.9 | 360.783 |
| plate4 | White | 3660003 | 408993.0 | 360.770 |
| plate5 | White | 3660011 | 408993.1 | 360.775 |
| plate6 | White | 3660019 | 408993.1 | 360.765 |
| GCP number | Latitude | Longitude |
|---|---|---|
| 1 | 33.07470 | -111.975 |
| 2 | 33.07478 | -111.975 |
| 3 | 33.07485 | -111.975 |
| 4 | 33.07492 | -111.975 |
| 5 | 33.07499 | -111.975 |
| 6 | 33.07506 | -111.975 |
GeoJSON files contain polygons that represent each plot in the gantry field (Figure @ref(fig:geojsonplot)). These polygons are used to extract smaller experimental units from larger units, such as the full field scale.
GeoJSON file containing a single polygon for each plot.
Our field design and dimensions remain pretty consistent from one season to the next. As a result, existing GeoJSONs are modified and applied to new seasons. In the case that a new GeoJSON needs to be created, please refer to FIELDimageR.
If you are editing a pre-existing GeoJSON, you will need to:
To move polygons, you need to load the GeoJSON and a drone orthomosaic onto QGIS. Then, you can follow the steps in Figure @ref(fig:geojsoneditplot):
Editing GeoJSON polygons using QGIS.
The “genotype” values in the GeoJSON file can be edited using GeoPandas. A GeoJSON can be opened up as a dataframe, similar to Pandas. Once opened, you can then replace the “genotype” columns using the fieldbook for the respective season. To see an example click here.